Whole genome sequencing (WGS), the process of determining the complete nucleotide or DNA/RNA sequence of a genome at one time, has made headlines recently for its potential to transform infectious disease management, particularly related to SARS-CoV-2, the virus responsible for the COVID-19 pandemic.

Patients at the greatest risk for secondary infections, particularly infections that are resistant to first-line antibiotics, include people who are already vulnerable due to other conditions and diseases—like COVID-19. Because of that, antimicrobial resistance poses a significant additional threat, especially as healthcare systems become overburdened.

It is estimated that one out of every twenty hospitalized patients will contract an HAI. These infections are a significant cause of illness and mortality, and are the source of serious economic consequences for the US health system each year.